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1
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1 ---
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2 output: html_document
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3 ---
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4
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5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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6 knitr::opts_chunk$set(
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7 echo = as.logical(opt$X_e),
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8 error = TRUE,
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9 eval = TRUE
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10 )
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11 ```
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12
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3
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13 ### Per tile sequence quality
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1
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14
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15 ```{r 'per tile sequence quality', fig.width=10}
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16 ## check if 'per tile sequence quality' module exits or not
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17 check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt')))
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18 if (length(check_ptsq) > 0) {
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19 ## reads 1
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20 ptsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per tile sequence quality')
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21 ptsq_1$trim = 'before'
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22
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23 ## reads 2
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24 ptsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per tile sequence quality')
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25 ptsq_2$trim = 'after'
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26
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27 comb_ptsq = rbind(ptsq_1, ptsq_2)
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28 comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim)
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29 comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base)
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30
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31 # convert integers to charaters
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3
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32 # comb_ptsq$Tile = as.character(comb_ptsq$X.Tile)
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1
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33
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3
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34 p = ggplot(data = comb_ptsq) +
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35 geom_raster(mapping = aes(x = Base, y = X.Tile, fill = Mean)) +
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1
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36 facet_grid(. ~ trim) +
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3
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37 scale_x_discrete(name = "Position in read (bp)") +
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38 scale_y_continuous(name = "") +
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39 scale_fill_gradient(low = "blue", high = "red") +
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40 theme(axis.text.x = element_text(size = 5, angle = 90),
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41 axis.text.y = element_text(size = 5),
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42 panel.background = element_rect(fill = NA))
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1
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43 ggplotly(p)
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44 } else {
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45 print('No "per tile sequence quality" data')
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46 }
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3
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47 ```
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